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The processive protease ClpAP translocates its substrate in discrete steps
Author(s) -
Jennings Laura D.,
Lun Desmond S.,
Medard Muriel,
Licht Stuart
Publication year - 2007
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.21.5.a273-c
Subject(s) - proteases , proteolysis , proteasome , protease , cleavage (geology) , biochemistry , chemistry , protein subunit , epitope , chromosomal translocation , microbiology and biotechnology , biology , enzyme , antigen , genetics , paleontology , fracture (geology) , gene
Processive proteases such as the bacterial Clp proteases and the mammalian proteasome serve two roles within the cell: degradation of misfolded proteins and (in mammalian cells) generation of antigenic peptides. Complete degradation of proteins requires processive proteolysis while antigen formation requires homogeneous pools of peptides of optimal length for epitope presentation (8–9 residues). Analysis of the ClpAP peptide product size distribution reveals a mechanism that could help optimize both the degradative and signaling functions of these proteases. Our data provides evidence that ClpAP translocates its substrate in discrete steps, indicating that it may share an unexpected mechanistic commonality with related ATPase‐driven motor proteins. Both size‐exclusion chromatography and MALDI mass spectrometry reveal a size distribution with pools of peptides at intervals corresponding to discrete steps in translocation. Our data support a model in which ClpAP translocates its substrates in 5–7 residue segments and, following each translocation step, the enzyme partitions between further translocation and proteolytic cleavage. Numerical simulations show that stepwise translocation enhances the ability of processive proteases to generate specific products of a defined length; use of this mechanism by mammalian proteasomes might account for the observed efficiency of epitope production. Funding by the MIT Chemistry Department.